Influenza viruses exchange segments of their genome when coinfecting the same cell, a process called reassortment. Reassortment generates significant diversity that can cause major epidemics and pandemics affecting a large proportion of the population. The basics of influenza virus reassortment are beginning to be uncovered, yet estimates of the frequency of reassortment in natural settings remain a major challenge. To address this need, this project will develop a high-throughput genotyping method that will enable precise quantification of reassortment in a wide variety of influenza A strains ata large scale and low cost. Specifically, this method will be used to study three major questions in influenza virus reassortment. During the mentored phase (K99) of this project, Dr. Diaz will enhance and adapt the genotyping tool he is currently developing for bacterial viruses to influenza in order to examine the relative roles of genetic similarity and geographic distance in promoting reassortment (Aim 1). To obtain a fuller picture of reassortment, this project will examine viral kinetics during experimental coinfections, which together with the relative reassortment rates, will allow an estimate of the total number of reassortants produced by coinfections (Aim 2). In the independent phase (R00), Dr. Diaz will use species distribution models of birds that are wild reservoirs of influenza to examine how reassortment in avian influenza strains is affected by host ecology (Aim 3). Collectively, these aims will meet Dr. Diaz' immediate goals to become a leading expert in influenza virus reassortment and to obtain a faculty position to pursue these questions. During the mentored phase of this project, Dr. Elodie Ghedin and Dr. David Gresham will train Dr. Diaz in the relevant methodologies in influenza virology, bioinformatics, and next-generation sequencing. Together with co-mentor Dr. Michael Purugganan, they will implement a career development plan, which will pave the way for Dr. Diaz' long term goal: to establish an independent, externally funded, and successful biomedical research laboratory on the forefront of contributing to the study of influenza coinfection and reassortment.